Thanks for the reply Peter33,
I was aware of that document, and I kind of managed to get the process to work by having a task that runs a VB Script on a continuous loop in the background just before the "Restart in Windows PE" task. The script would keep running the command to reset the MBR. However on the odd occasion this would fail and I would end up with an unbootable HDD on reboot.
In that document I want to try and achieve what they are suggesting in appendix C part 2a. This would guarantee that the process would always work because I could get the command to restore the MBR to occur exactly after the WinPE image has been staged into the MBR, but before the reboot.